White House Chief of Staff John Kelly knew that President Donald Trump’s staff secretary had issues in his past possibly impeding a permanent security clearance before news reports this week on domestic violence allegations against the aide, people familiar with the matter said.

White House Chief of Staff John Kelly and Staff Secretary Rob Porter on Nov. 29, 2017.

Photographer: Jabin Botsford/The Washington Post via Getty Images

A deputy chief of staff, Joe Hagin, was concerned that Rob Porter hadn’t yet passed a background check more than a year into his tenure and briefed his boss, Kelly, the people said. Porter continued in his high-level job while his bosses waited for the conclusion of the staff secretary’s security clearance investigation, the people said.

Kelly and Hagin didn’t know the specific allegations against the staff secretary, the people said. Kelly asked Hagin a few weeks ago to dig deeper into why there had been delays in background checks of certain key staff, including Porter. Meanwhile, the Porter that Kelly and other top staff saw every day at the White House was excellent at his job and cordial to his colleagues.

“Kelly became fully aware about these allegations yesterday,” Deputy White House Press Secretary Raj Shah told reporters at the White House on Thursday. “I’m not going to get into specifics about who may have known what pieces of information.”

The episode is another staffing embarrassment for Trump and may threaten Kelly’s standing in the White House. Several aides and White House advisers expressed disgust and said Kelly had failed the president if he knew about Porter’s history with his ex-wives and didn’t inform Trump.

After issuing a complimentary statement on Porter earlier on Wednesday, Kelly said in the evening that he “was shocked by the new allegations released today. There is no place for domestic violence in our society.”

Trump didn’t know about Porter’s history with the two ex-wives before Tuesday, when the DailyMail.com approached the White House with details of an interview with one of the women, two White House officials said.

“He was saddened for all of the individuals involved,” Shah said.

Porter announced on Wednesday he would resign but without leaving the White House immediately. Realization about the seriousness of the abuse allegations grew within the White House after The Intercept published an interview with a second ex-wife and a photo of what she said was a black eye inflicted by Porter.

He denied both of the ex-wives’ allegations. His last day at the White House is now today.

“The allegations against Rob Porter are serious and deeply troubling,” Shah said. “He did deny them. The incidents took place long before he joined the White House.”

Rob Porter

Photographer: Nicholas Kamm/AFP via Getty Images

Porter’s title understates his significance in the White House. He served as a clearinghouse for paperwork coming in or out of the Oval Office, and he was an important influence on policy in his own right. Few aides enjoyed greater access to the Oval Office, or spent more time in the president’s company. He also played a vital role in helping Kelly try to bring order to the White House.

Trump didn’t mention Porter when he gathered with lawmakers, members of the military and former Vice President Dick Cheney at the White House on Tuesday evening to watch the movie “12 Strong.” Porter’s situation wasn’t discussed in the White House’s senior staff meeting on Wednesday led by chief of staff John Kelly, but it was addressed in smaller groups, aides said.

Security Clearance

Allegations of domestic violence can be grounds for the government to deny security clearances to aspiring officials. Yet Porter had sat in on meetings of the National Security Council where top secret matters were discussed, according to three people familiar with the situation. Someone in his position would have had an interim clearance while the FBI conducted a background check, according to one official.

Senior staff at the White House apply for five-year clearances, and the process can be lengthy -- some current officials are still waiting, aides said. Porter never received a permanent clearance and his background investigation was ongoing when he resigned, Shah said.

“The fact that Porter might have held a senior White House position without a security clearance is troubling and merits a full investigation,” said Chris Lu, former cabinet secretary under President Barack Obama and senior fellow at the University of Virginia Miller Center. “I’ve lost count as to how many Trump appointees have​ been sidelined because of their past views or conduct​. But​ this is further evidence of a non-existent vetting process.”

Given the allegations made by his former wives, who The Intercept said were both interviewed by the FBI as part of Porter’s background check, some White House aides said they too were disturbed that he had access to top secret information.

All of the officials interviewed for this story requested anonymity to discuss a personnel and national security matter.

Top Secret SCI

A president’s staff secretary typically would be cleared at a level of security called Top Secret Sensitive Compartmented Information, allowing the aide to handle extremely sensitive information, according to a former White House official with knowledge of the process. The secretary would have access to two computer systems, one classified and the other unclassified, the former official said.

Staff secretaries are also typically privy to information in the classified President’s Daily Briefing, a summary of intelligence on threats to the U.S., the former official said.

Porter’s ex-wife, Jennifer Willoughby, told the DailyMail.com -- the U.S. website of a U.K. tabloid -- that he had difficulty controlling his anger and at one point pulled her out of the shower and yelled at her. She took out the protective order against him in after he allegedly violated a separation agreement and punched through glass in the door of their home, cutting himself. The website published a copy of the order.

Porter’s other ex-wife, Colbie Holderness, provided a brief statement to DailyMail.com alleging Porter had abused her, but the website didn’t detail her claims. The Intercept published its interview with Holderness on Wednesday.

Some White House aides were particularly disturbed by the photo The Intercept published of Holderness with a black eye. She told the publication Porter punched her while they were on vacation.

Porter called the allegations “outrageous” and “simply false.” In a statement, he said he had taken the pictures that Holderness provided to The Intercept and that “the reality behind them is nowhere close to what is being described.”

“I have always put duty to country first and treated others with respect,” Porter said in a statement. “I am deeply grateful for the opportunity to have served in the Trump administration and will seek to ensure a smooth transition when I leave the White House.”

Holderness did not respond to attempts to contact her by telephone and email.

Kelly Statement

Kelly’s first statement on Porter complimented him without mentioning the allegations.

“Rob Porter is a man of true integrity and honor and I can’t say enough good things about him,” Kelly said. “He is a friend, a confidante and a trusted professional. I am proud to serve alongside him.”

Several White House aides said Wednesday that Kelly’s statement was a mistake. But Kelly has leaned heavily on Porter since becoming chief of staff in July, and considers the staff secretary to be a close and trusted confidante, they said.

The Daily Mail has recently delved into Porter’s personal life, reporting last week -- complete with paparazzi-style photos -- that he was in a romantic relationship with another of Trump’s most senior aides, White House Communications Director Hope Hicks.

Kelly assigned Porter to help bring more discipline to the West Wing by ensuring that no staff memos, policy documents, correspondence or news articles reached Trump’s desk without careful inspection. He almost always accompanied the president when he traveled, and frequently could be seen near Trump as he boarded Marine One and Air Force One.

He was one of a handful of aides who helped to write the president’s first State of the Union address. As an assistant to the president, Porter was paid the top White House staff salary of $179,000.